Abstract:
In southern Africa, clade 2.3.4.4B H5N1 high pathogenicity avian influenza (HPAI) was
first detected in South African (SA) poultry in April 2021, followed by outbreaks in poultry or wild
birds in Lesotho and Botswana. In this study, the complete or partial genomes of 117 viruses from the
SA outbreaks in 2021–2022 were analyzed to decipher the sub-regional spread of the disease. Our
analysis showed that seven H5N1 sub-genotypes were associated with the initial outbreaks, but by
late 2022 only two sub-genotypes still circulated. Furthermore, SA poultry was not the source of
Lesotho’s outbreaks, and the latter was most likely an introduction from wild birds. Similarly, SA and
Botswana’s outbreaks in 2021 were unrelated, but viruses of Botswana’s unique sub-genotype were
introduced into SA later in 2022 causing an outbreak in ostriches. At least 83% of SA’s commercial
poultry cases in 2021–2022 were point introductions from wild birds. Like H5N8 HPAI in 2017–2018, a
coastal seabird-restricted sub-lineage of H5N1 viruses emerged in the Western Cape province in 2021
and spread to Namibia, causing mortalities in Cape Cormorants. In SA ~24,000 of this endangered
species died, and the loss of >300 endangered African penguins further threatens biodiversity.
